Place chicken thighs and chicken breasts in a slow cooker. Whisk red wine vinegar, green onions, lime juice, and garlic together in a bowl; pour over chicken.
Cook on High for 4 hours.
Blend sour cream, chipotle peppers in adobo sauce, and 1/4 teaspoon salt together in a food processor until sauce is smooth; refrigerate until ready to use.
Place chicken on a work surface and shred into bite-size chunks; season with salt and pepper. Measure 1/2 cup cooking liquid in slow cooker and discard the rest. Return shredded chicken and 1/2 cup cooking liquid to slow cooker and add cilantro; cook and stir until chicken is heated through, about 5 minutes.
Spoon chicken into tortillas and top with chipotle cream sauce.